Rob,
this is one of the things I'm not really happy on.
I never seen DNN 3.2.0, 3.2.1, 4.0.0 or DNN 4.0.1 before the official release, so I can not take care of any changes which was done in the core product.
As far as this situation is not solved in general for the dotnetnuke sub projects I would recommend only to make an upgrade of your portal if you are using only the default modules which are included in the install\modules folder of the install version.
For any additional modules (like blog, forum ...) it would be the best to wait for the announcement that the version is tested with a specific core version.
I know that this is not really a friendly solution, but I don't have any other idea how we (the sub project leader and member) should be able to give you the necessary support for a DotNetNuke sub project.
regards
HP